Many pharmaceutical agents work by covalently binding to nucleophiles found on their molecular targets in vivo. For example, enzyme inhibitors are frequently designed to target and covalently bind to nucleophiles (e.g., thiols of cysteines, hydroxyl groups of serine, threonine, or tyrosine) in the active site of the enzyme. Functional groups that bond covalently to active site nucleophiles, therefore, frequently form the basis for the design of potent and selective enzyme inhibitors. Those functional groups that form covalent bonds reversibly (e.g., carbonyl groups, boronic esters) are especially valuable in pharmaceutical development (for leading references, please see Adams, J. Curr. Opin. Chem. Biol. 6:493, 2002, Lecaille et al. Chem. Rev. 102:4459, 2002; each of which is incorporated herein by reference).

Avrainvillamide and stephacidin B, formally a dimer of avrainvillamide, have recently been identified and have been shown to include a 3-alkylidene-3H-indole 1-oxide group, which is capable of reversible covalent modification of a heteroatom-based nucleophile. Both of these compounds have been separately identified in culture media from various strains of Aspergillus (for the isolation of avrainvillamide, see Fenical et al. U.S. Pat. No. 6,066,635, issued May 23, 2000; Sugie et al. J. Antibiot. 54:911, 2001; each of which is incorporated herein by reference; for the isolation of stephacidins A and B, see Qian-Cutrone et al. J. Am. Chem. Soc. 124:14556, 2002; Qian-Cutrone et al., U.S. Pat. No. 6,291,461, 2003; each of which is incorporated herein by reference). Both compounds exhibit anti-proliferative activity (IC50 values ˜50-100 nM), and avrainvillamide has been reported to exhibit anti-microbial activity against multidrug-resistant bacteria. These compounds are apparently the first natural product with a 3-alkylidene-3H-indole 1-oxide functional group.
Crystallization and x-ray analysis has been used to establish the structure of stephacidin B. It has now been recognized that stephacidin B is formed by the dimerization of avrainvillamide. A mechanism for the putative dimerization reaction was advanced that involved the protonation of avrainvillamide followed by formation of bonds b and a, in that order, via cationic intermediates (Qian-Cutrone et al. J. Am. Chem. Soc. 124:14556, 2002; incorporated herein by reference).
Given the biological activity of these newly isolated natural products, a synthetic route for preparing these compounds and analogs of these compounds would be useful in designing new therapeutics and investigating the structure-activity relationship of these compounds.